Bioinformatics Identification And Evolutionary Analysis Of Cucumber

Long noncoding RNAs (lncRNAs) that have a length more than 200 nt and lack coding potential is a novel RNA found in recent years. They can regulate gene expression at the transcriptional and post-transcriptional levels by acting as signals, decoys, guides, and scaffolds, and participate in many biology processes, such as reproduce, growth, cell differentiation, cell-recycle regulation, cancinogenesis. Based on the location in genome, lncRNAs can be divided into intergenic lncRNAs (lincRNAs), intron lncRNAs, antisense lncRNAs, etc.LincRNAs is a kind of lncRNAs distributing in the intergenetic region of genome. Comparing with animals, studies of lincRNAs in plants has received less attention, only several plants like Arabidosis, maize, rice, millet, sorghum having been investigated for the system identification of lincRNAs in genome-wide. Evidences show that lincRNAs are import in processes of response to biotic or abiotic stresses. Besides, plant lincRNAs also play multiple roles by producing miRNAs or acting as targets or target mimics of miRNAs. In spite of this, the ways of action, the mechanisms and functions of plant lincRNAs all need to be studied forward.Cucumber is an important vegetable economic plant, which can be used as a model to analyze lincRNAs due to its import as a model plant for studying sex differentiation, fruit development, and vascular transport. Many genomes and transcriptoms of cucumber are available, which make it possible for the identification, functional analysis of lincRNAs in cucumber. To obtain lincRNAs systematically and their potential regulation mechanisms, functions and evolution, we designed a bioinformatics pipeline, which integrated several tools and analysis against database, including location filters, ORF and length filter, coding potential filter. We first use the pipeline to identify cucumber lincRNAs systematically. Our results show that:1. Sequence and expression analysis. Cucumber lincRNAs have high conserve level among relative species, but have low conserve level among distance species. Expression shows that cucumber lincRNAs have a low expression levels among each tissues than that of protein coding RNAs, and cucumber lincRNAs show tissue-specific expression and have the most number lincRNAs, for the tissue-specific expression,2. The mechanisms of lincRNAs. Coexpression network shows that 388 lincRNAs are coexpressing with 2347 mRNAs, which suggest the potential regulating between lincRNAs and mRNAs. The analysis between miRNAs and lincRNAs shows that 17 miNRAs can target 10 cucumber lincRNAs. The result shows that cucumber lincRNAs can work as targets of miRNAs and join in the regulation of miRNAs.3. The function analysis.96 lincRNAs were annotated, which may response to endogenous stimulus, response to chemical stimulus, response to temperature stimulus, and join in small molecule metabolic process, secondary metabolic process, carbohydrate metabolic process, oxidation-reduction process.4. Evolution analysis of lincRNAs.11,923 SNPs are found in lincRNAs among 102 cucumber accessions. The average Pi is 0.00079439+/-0.001338246. Further analysis shows that lincRNAs have a low diversity. Molecular evolution analysis shows that most lincRNAs possess negative tajima’s D value, and 81 lincRNAs display a significant probability (P<0.05) of non-neutral patterns of sequence variation. Further analysis shows that at least 16 of the lincRNAs with a significant Tajima’s D might be a result of selection.Result:We identify and characterize 3,274 lincRNAs, which make the lincRNA source more rich. The found of mechanism that cucumber lincRNAs can be regulated by miRNAs is good to further study the regulation between cucumber lincRNAs and miRNAs. Based on the co-expression analysis of lincRNAs and mRNAs,94 lincRNAs were annotated, which may response to stimuli, multi-organism processes, reproduction, multi-organism processes, and growth. Examination of the evolution of lincRNAs showed that most lincRNAs are under purifying selection, even some lincRNAs are under positive selection.